Starting phenix.real_space_refine
on Thu Sep 18 10:45:35 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9ne7_49300/09_2025/9ne7_49300.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ne7_49300/09_2025/9ne7_49300.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ne7_49300/09_2025/9ne7_49300.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ne7_49300/09_2025/9ne7_49300.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ne7_49300/09_2025/9ne7_49300.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ne7_49300/09_2025/9ne7_49300.map"
  }
  resolution = 3.53
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     P      41      5.49       5
     S     102      5.16       5
     C   10097      2.51       5
     N    2715      2.21       5
     O    3179      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16138
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 9265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1138, 9265
          Classifications: {'peptide': 1138}
          Link IDs: {'PTRANS': 58, 'TRANS': 1079}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2008
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 7, 'TRANS': 253}
    Chain: "C"
      Number of atoms: 2008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2008
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 7, 'TRANS': 253}
    Chain: "D"
      Number of atoms: 2008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2008
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 7, 'TRANS': 253}
    Chain: "P"
      Number of atoms: 412
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 412
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
    Chain: "T"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 429
          Classifications: {'DNA': 21}
          Link IDs: {'rna3p': 20}
    Chain: "A"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'SF4': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   4815  SG  CYS A 651      42.278  85.068  91.366  1.00 90.05           S
  ATOM   4831  SG  CYS A 654      40.866  87.199  97.141  1.00 90.00           S
  ATOM   4897  SG  CYS A 663      46.576  89.069  94.280  1.00 84.84           S
  ATOM   5621  SG  CYS A 747      45.831  83.259  96.161  1.00 65.79           S

  Time building chain proxies: 4.08, per 1000 atoms: 0.25
  Number of scatterers: 16138
  At special positions: 0
  Unit cell: (103.5, 110.124, 142.416, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      4     26.01
     S     102     16.00
     P      41     15.00
     O    3179      8.00
     N    2715      7.00
     C   10097      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.23
  Conformation dependent library (CDL) restraints added in 627.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" SF4 A1301 "
        pdb="FE4  SF4 A1301 " - pdb=" SG  CYS A 747 "
        pdb="FE3  SF4 A1301 " - pdb=" SG  CYS A 663 "
        pdb="FE2  SF4 A1301 " - pdb=" SG  CYS A 654 "
        pdb="FE1  SF4 A1301 " - pdb=" SG  CYS A 651 "
      Number of angles added : 12


  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3656

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 20 sheets defined
      34.4% alpha, 21.3% beta
      18 base pairs and 33 stacking pairs defined.
    Time for finding SS restraints: 2.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 47
      removed outlier: 5.232A  pdb=" N   GLU A  36 " --> pdb=" O   LEU A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 122
    Processing helix  chain 'A' and resid 159 through 181
      Proline residue:  A 172  - end of helix
      removed outlier: 3.628A  pdb=" N   ASP A 181 " --> pdb=" O   ASN A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 216
      No H-bonds generated for 'chain 'A' and resid 214 through 216'
    Processing helix  chain 'A' and resid 227 through 236
    Processing helix  chain 'A' and resid 339 through 355
    Processing helix  chain 'A' and resid 368 through 379
    Processing helix  chain 'A' and resid 407 through 414
    Processing helix  chain 'A' and resid 418 through 422
    Processing helix  chain 'A' and resid 425 through 431
    Processing helix  chain 'A' and resid 440 through 451
      removed outlier: 3.559A  pdb=" N   MET A 444 " --> pdb=" O   ASP A 440 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   CYS A 445 " --> pdb=" O   PRO A 441 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   ARG A 446 " --> pdb=" O   GLU A 442 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   THR A 449 " --> pdb=" O   CYS A 445 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   GLU A 450 " --> pdb=" O   ARG A 446 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   GLN A 451 " --> pdb=" O   MET A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 473
      removed outlier: 3.607A  pdb=" N   TYR A 473 " --> pdb=" O   LEU A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 482
    Processing helix  chain 'A' and resid 488 through 495
      removed outlier: 3.620A  pdb=" N   LYS A 495 " --> pdb=" O   GLU A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 512
      removed outlier: 3.627A  pdb=" N   LEU A 500 " --> pdb=" O   GLY A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 572
    Processing helix  chain 'A' and resid 573 through 585
    Processing helix  chain 'A' and resid 589 through 593
      removed outlier: 4.271A  pdb=" N   GLN A 592 " --> pdb=" O   PRO A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 612
    Processing helix  chain 'A' and resid 629 through 638
    Processing helix  chain 'A' and resid 647 through 652
      removed outlier: 3.563A  pdb=" N   CYS A 651 " --> pdb=" O   ASP A 647 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ALA A 652 " --> pdb=" O   GLU A 648 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 647 through 652'
    Processing helix  chain 'A' and resid 679 through 690
    Processing helix  chain 'A' and resid 711 through 731
      removed outlier: 3.920A  pdb=" N   LYS A 729 " --> pdb=" O   ASP A 725 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 753 through 786
    Processing helix  chain 'A' and resid 787 through 820
      removed outlier: 4.616A  pdb=" N   TYR A 816 " --> pdb=" O   LEU A 812 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   GLY A 817 " --> pdb=" O   ASN A 813 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   VAL A 819 " --> pdb=" O   PHE A 815 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   MET A 820 " --> pdb=" O   TYR A 816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 828 through 854
      removed outlier: 3.889A  pdb=" N   ALA A 832 " --> pdb=" O   SER A 828 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 892 through 905
    Processing helix  chain 'A' and resid 982 through 993
    Processing helix  chain 'A' and resid 998 through 1019
      removed outlier: 3.838A  pdb=" N   TYR A1012 " --> pdb=" O   LYS A1008 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   TRP A1013 " --> pdb=" O   VAL A1009 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1028 through 1034
    Processing helix  chain 'A' and resid 1052 through 1062
    Processing helix  chain 'A' and resid 1065 through 1069
      removed outlier: 3.970A  pdb=" N   MET A1068 " --> pdb=" O   GLY A1065 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1102 through 1114
      removed outlier: 3.811A  pdb=" N   LEU A1114 " --> pdb=" O   LEU A1110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1123 through 1128
      removed outlier: 4.018A  pdb=" N   LEU A1128 " --> pdb=" O   ILE A1124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1129 through 1145
      removed outlier: 3.598A  pdb=" N   TYR A1133 " --> pdb=" O   ASP A1129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1152
    Processing helix  chain 'A' and resid 1164 through 1176
    Processing helix  chain 'B' and resid 9 through 19
      removed outlier: 3.919A  pdb=" N   LEU B  19 " --> pdb=" O   VAL B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 82
      removed outlier: 3.630A  pdb=" N   MET B  75 " --> pdb=" O   ASN B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 155
    Processing helix  chain 'B' and resid 209 through 217
    Processing helix  chain 'B' and resid 218 through 222
      removed outlier: 3.833A  pdb=" N   SER B 222 " --> pdb=" O   THR B 219 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 9 through 23
      removed outlier: 3.538A  pdb=" N   LYS C  13 " --> pdb=" O   GLY C   9 " (cutoff:3.500A)
      removed outlier: 5.113A  pdb=" N   ASP C  21 " --> pdb=" O   GLU C  17 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   LEU C  22 " --> pdb=" O   ALA C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 55 through 57
      No H-bonds generated for 'chain 'C' and resid 55 through 57'
    Processing helix  chain 'C' and resid 71 through 80
      removed outlier: 3.772A  pdb=" N   MET C  75 " --> pdb=" O   ASN C  71 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   LYS C  77 " --> pdb=" O   THR C  73 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ILE C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 141 through 153
      removed outlier: 3.514A  pdb=" N   HIS C 153 " --> pdb=" O   ARG C 149 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 216
    Processing helix  chain 'C' and resid 217 through 222
      Proline residue:  C 220  - end of helix
      No H-bonds generated for 'chain 'C' and resid 217 through 222'
    Processing helix  chain 'D' and resid 9 through 20
      removed outlier: 3.576A  pdb=" N   LYS D  13 " --> pdb=" O   GLY D   9 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 57
      No H-bonds generated for 'chain 'D' and resid 55 through 57'
    Processing helix  chain 'D' and resid 72 through 80
    Processing helix  chain 'D' and resid 141 through 153
      removed outlier: 3.910A  pdb=" N   HIS D 153 " --> pdb=" O   ARG D 149 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 217
      removed outlier: 3.723A  pdb=" N   LEU D 212 " --> pdb=" O   ALA D 208 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   LYS D 217 " --> pdb=" O   ASN D 213 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 218 through 222
    Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 70
    Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 70
      removed outlier: 3.827A  pdb=" N   ASN A  65 " --> pdb=" O   TYR A  85 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   ILE A  87 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
      removed outlier: 5.517A  pdb=" N   LEU A  63 " --> pdb=" O   ILE A  87 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   TRP A 243 " --> pdb=" O   ARG A 260 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 136
      removed outlier: 3.826A  pdb=" N   LYS A 130 " --> pdb=" O   SER A 156 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   LYS A 136 " --> pdb=" O   ARG A 150 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ARG A 150 " --> pdb=" O   LYS A 136 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ASN A 151 " --> pdb=" O   THR A 108 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   THR A 108 " --> pdb=" O   ASN A 151 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU A 155 " --> pdb=" O   PHE A 104 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   PHE A 104 " --> pdb=" O   LEU A 155 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   TYR A 105 " --> pdb=" O   MET A 221 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   MET A 221 " --> pdb=" O   TYR A 105 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   ALA A 107 " --> pdb=" O   VAL A 219 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 278
      removed outlier: 3.741A  pdb=" N   SER A 297 " --> pdb=" O   ALA A 275 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ALA A 277 " --> pdb=" O   MET A 295 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   MET A 295 " --> pdb=" O   ALA A 277 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   MET A 294 " --> pdb=" O   ASN A 309 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   PHE A 335 " --> pdb=" O   GLY A 304 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   LEU A 306 " --> pdb=" O   PHE A 335 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   GLU A 337 " --> pdb=" O   LEU A 306 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   THR A 308 " --> pdb=" O   GLU A 337 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 358 through 361
    Processing sheet with id=AA6, first strand: chain 'A' and resid 390 through 391
      removed outlier: 3.906A  pdb=" N   GLN A 390 " --> pdb=" O   LYS A 398 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LYS A 398 " --> pdb=" O   GLN A 390 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 534 through 539
      removed outlier: 6.763A  pdb=" N   GLU A 674 " --> pdb=" O   ASP A 535 " (cutoff:3.500A)
      removed outlier: 5.008A  pdb=" N   GLU A 537 " --> pdb=" O   ARG A 672 " (cutoff:3.500A)
      removed outlier: 7.291A  pdb=" N   ARG A 672 " --> pdb=" O   GLU A 537 " (cutoff:3.500A)
      removed outlier: 5.145A  pdb=" N   TYR A 539 " --> pdb=" O   GLN A 670 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   GLN A 670 " --> pdb=" O   TYR A 539 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   MET A 667 " --> pdb=" O   THR A 744 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   THR A 744 " --> pdb=" O   MET A 667 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 545 through 546
      removed outlier: 3.502A  pdb=" N   ARG A 855 " --> pdb=" O   VAL A 867 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   TRP A 865 " --> pdb=" O   LEU A 857 " (cutoff:3.500A)
      removed outlier: 5.160A  pdb=" N   LEU A 859 " --> pdb=" O   GLY A 863 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   GLY A 863 " --> pdb=" O   LEU A 859 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 550 through 553
      removed outlier: 4.123A  pdb=" N   ALA A 939 " --> pdb=" O   PHE A 959 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 875 through 879
    Processing sheet with id=AB2, first strand: chain 'A' and resid 911 through 915
      removed outlier: 7.428A  pdb=" N   THR A 920 " --> pdb=" O   ALA A 914 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1079 through 1080
      removed outlier: 3.550A  pdb=" N   ILE A1079 " --> pdb=" O   ILE A1094 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ILE A1094 " --> pdb=" O   ILE A1079 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1189 through 1191
      removed outlier: 4.041A  pdb=" N   GLY A1191 " --> pdb=" O   GLN D 125 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   GLN D 125 " --> pdb=" O   GLY A1191 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 59 through 61
      removed outlier: 3.619A  pdb=" N   ALA B   4 " --> pdb=" O   LEU B  90 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL C 167 " --> pdb=" O   LEU C 182 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   SER C 172 " --> pdb=" O   ALA C 157 " (cutoff:3.500A)
      removed outlier: 5.220A  pdb=" N   ALA C 157 " --> pdb=" O   SER C 172 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU C 205 " --> pdb=" O   ILE C 160 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 66 through 68
      removed outlier: 3.819A  pdb=" N   SER B  39 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   VAL B  48 " --> pdb=" O   SER B  39 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   GLN B  49 " --> pdb=" O   LYS B 248 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU B 247 " --> pdb=" O   TYR B 239 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   LYS B 240 " --> pdb=" O   THR B 224 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   THR B 224 " --> pdb=" O   LYS B 240 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   MET B 229 " --> pdb=" O   CYS B 135 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL B 136 " --> pdb=" O   GLU B 198 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 204 through 208
      removed outlier: 3.654A  pdb=" N   LEU B 205 " --> pdb=" O   ILE B 160 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   VAL B 158 " --> pdb=" O   PHE B 207 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   ALA B 157 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   SER B 172 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ASP D 113 " --> pdb=" O   ASN B 179 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ILE D  88 " --> pdb=" O   LEU D   6 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 59 through 61
      removed outlier: 4.356A  pdb=" N   THR C  59 " --> pdb=" O   ARG C   5 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLU C   3 " --> pdb=" O   ARG C  61 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU C  99 " --> pdb=" O   MET C 116 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ASN D 177 " --> pdb=" O   GLU C 115 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   VAL D 167 " --> pdb=" O   LEU D 182 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   SER D 172 " --> pdb=" O   ALA D 157 " (cutoff:3.500A)
      removed outlier: 4.873A  pdb=" N   ALA D 157 " --> pdb=" O   SER D 172 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU D 205 " --> pdb=" O   ILE D 160 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 66 through 67
      removed outlier: 3.516A  pdb=" N   TYR C 250 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR C  51 " --> pdb=" O   HIS C 246 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   TYR C 249 " --> pdb=" O   VAL C 237 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU C 251 " --> pdb=" O   LEU C 235 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU C 235 " --> pdb=" O   LEU C 251 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU C 227 " --> pdb=" O   VAL C 137 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 66 through 71
    Processing sheet with id=AC2, first strand: chain 'D' and resid 196 through 198
      removed outlier: 3.619A  pdb=" N   THR D 196 " --> pdb=" O   LYS D 138 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   THR D 226 " --> pdb=" O   GLU D 238 " (cutoff:3.500A)

    686 hydrogen bonds defined for protein.
    1944 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      42 hydrogen bonds
      84 hydrogen bond angles
      0 basepair planarities
      18 basepair parallelities
      33 stacking parallelities
  Total time for adding SS restraints: 3.38

  Time building geometry restraints manager: 1.72 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.43: 6929
        1.43 -     1.64: 9438
        1.64 -     1.86: 158
        1.86 -     2.07: 0
        2.07 -     2.28: 12
  Bond restraints: 16537
  Sorted by residual:
  bond pdb=" C3'  DT T  14 "
       pdb=" O3'  DT T  14 "
    ideal  model  delta    sigma   weight residual
    1.422  1.467 -0.045 3.00e-02 1.11e+03 2.25e+00
  bond pdb=" CA  ILE A1147 "
       pdb=" CB  ILE A1147 "
    ideal  model  delta    sigma   weight residual
    1.539  1.547 -0.008 5.40e-03 3.43e+04 2.14e+00
  bond pdb=" CB  MET A 831 "
       pdb=" CG  MET A 831 "
    ideal  model  delta    sigma   weight residual
    1.520  1.481  0.039 3.00e-02 1.11e+03 1.67e+00
  bond pdb=" CA  ARG B  64 "
       pdb=" CB  ARG B  64 "
    ideal  model  delta    sigma   weight residual
    1.534  1.554 -0.021 1.64e-02 3.72e+03 1.61e+00
  bond pdb=" CG1 ILE A 296 "
       pdb=" CD1 ILE A 296 "
    ideal  model  delta    sigma   weight residual
    1.513  1.467  0.046 3.90e-02 6.57e+02 1.38e+00
  ... (remaining 16532 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 21686
        1.89 -     3.78: 693
        3.78 -     5.67: 93
        5.67 -     7.56: 36
        7.56 -     9.44: 12
  Bond angle restraints: 22520
  Sorted by residual:
  angle pdb=" C   ALA A1022 "
        pdb=" CA  ALA A1022 "
        pdb=" CB  ALA A1022 "
      ideal   model   delta    sigma   weight residual
     116.63  110.20    6.43 1.16e+00 7.43e-01 3.08e+01
  angle pdb=" N   ASP B 243 "
        pdb=" CA  ASP B 243 "
        pdb=" C   ASP B 243 "
      ideal   model   delta    sigma   weight residual
     110.44  104.10    6.34 1.20e+00 6.94e-01 2.79e+01
  angle pdb=" C   LEU A 424 "
        pdb=" N   LYS A 425 "
        pdb=" CA  LYS A 425 "
      ideal   model   delta    sigma   weight residual
     121.54  130.32   -8.78 1.91e+00 2.74e-01 2.11e+01
  angle pdb=" C   TYR A 731 "
        pdb=" N   LYS A 732 "
        pdb=" CA  LYS A 732 "
      ideal   model   delta    sigma   weight residual
     121.54  129.46   -7.92 1.91e+00 2.74e-01 1.72e+01
  angle pdb=" CA  ARG A 579 "
        pdb=" CB  ARG A 579 "
        pdb=" CG  ARG A 579 "
      ideal   model   delta    sigma   weight residual
     114.10  122.06   -7.96 2.00e+00 2.50e-01 1.58e+01
  ... (remaining 22515 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.62: 9420
       28.62 -    57.24: 524
       57.24 -    85.86: 66
       85.86 -   114.48: 4
      114.48 -   143.10: 1
  Dihedral angle restraints: 10015
    sinusoidal: 4374
      harmonic: 5641
  Sorted by residual:
  dihedral pdb=" CA  MET A 359 "
           pdb=" C   MET A 359 "
           pdb=" N   VAL A 360 "
           pdb=" CA  VAL A 360 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.12  -25.88     0      5.00e+00 4.00e-02 2.68e+01
  dihedral pdb=" CA  PRO D 253 "
           pdb=" C   PRO D 253 "
           pdb=" N   LYS D 254 "
           pdb=" CA  LYS D 254 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.45   23.55     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" CA  ASN C  71 "
           pdb=" C   ASN C  71 "
           pdb=" N   LEU C  72 "
           pdb=" CA  LEU C  72 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.14  -20.86     0      5.00e+00 4.00e-02 1.74e+01
  ... (remaining 10012 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1925
       0.053 -    0.106: 483
       0.106 -    0.159: 91
       0.159 -    0.212: 9
       0.212 -    0.265: 3
  Chirality restraints: 2511
  Sorted by residual:
  chirality pdb=" CB  THR A 528 "
            pdb=" CA  THR A 528 "
            pdb=" OG1 THR A 528 "
            pdb=" CG2 THR A 528 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.29    0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CB  ILE A 296 "
            pdb=" CA  ILE A 296 "
            pdb=" CG1 ILE A 296 "
            pdb=" CG2 ILE A 296 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CA  THR C 219 "
            pdb=" N   THR C 219 "
            pdb=" C   THR C 219 "
            pdb=" CB  THR C 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.31    0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 2508 not shown)

  Planarity restraints: 2762
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 425 "    0.017 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        pdb=" C   LYS A 425 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   LYS A 425 "    0.022 2.00e-02 2.50e+03
        pdb=" N   ALA A 426 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 613 "    0.044 5.00e-02 4.00e+02   6.68e-02 7.14e+00
        pdb=" N   PRO A 614 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A 614 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 614 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 330 "   -0.040 5.00e-02 4.00e+02   6.01e-02 5.78e+00
        pdb=" N   PRO A 331 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A 331 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 331 "   -0.033 5.00e-02 4.00e+02
  ... (remaining 2759 not shown)

  Histogram of nonbonded interaction distances:
        2.60 -     3.06: 9825
        3.06 -     3.52: 17086
        3.52 -     3.98: 24841
        3.98 -     4.44: 28659
        4.44 -     4.90: 44839
  Nonbonded interactions: 125250
  Sorted by model distance:
  nonbonded pdb=" N1   DG P  26 "
            pdb=" C4   DG P  26 "
     model   vdw
     2.600 2.672
  nonbonded pdb=" N1   DG T  15 "
            pdb=" C4   DG T  15 "
     model   vdw
     2.602 2.672
  nonbonded pdb=" N1   DG P  14 "
            pdb=" C4   DG P  14 "
     model   vdw
     2.602 2.672
  nonbonded pdb=" N1   DG P  17 "
            pdb=" C4   DG P  17 "
     model   vdw
     2.602 2.672
  nonbonded pdb=" N1   DG P  20 "
            pdb=" C4   DG P  20 "
     model   vdw
     2.603 2.672
  ... (remaining 125245 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     19.820
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6957
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  16541  Z= 0.178
  Angle     :  0.827  14.598  22532  Z= 0.424
  Chirality :  0.049   0.265   2511
  Planarity :  0.006   0.067   2762
  Dihedral  : 16.927 143.101   6359
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.45 (0.18), residues: 1911
  helix: -0.63 (0.20), residues: 579
  sheet: -0.42 (0.24), residues: 485
  loop : -1.44 (0.19), residues: 847

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 375 
 TYR   0.018   0.002   TYR A 362 
 PHE   0.030   0.002   PHE A 815 
 TRP   0.037   0.002   TRP A 369 
 HIS   0.008   0.001   HIS B 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (16537)
  covalent geometry    : angle       0.80521 (22520)
  hydrogen bonds       : bond        0.18832 (  726)
  hydrogen bonds       : angle       7.98847 ( 2028)
  metal coordination   : bond        0.01113 (    4)
  metal coordination   : angle       8.25920 (   12)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 334
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.7853 (mp) cc_final: 0.7472 (pp)
REVERT: A  132 GLU cc_start: 0.6843 (pm20) cc_final: 0.6384 (pm20)
REVERT: A  223 GLU cc_start: 0.7690 (pm20) cc_final: 0.6267 (pm20)
REVERT: A  294 MET cc_start: 0.5686 (pmm) cc_final: 0.4570 (ptm)
REVERT: A  446 ARG cc_start: 0.6898 (tmm160) cc_final: 0.6498 (mmt180)
REVERT: A  689 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8490 (pt0)
REVERT: A  740 GLU cc_start: 0.6993 (pt0) cc_final: 0.6699 (pp20)
REVERT: A  850 ILE cc_start: 0.8568 (mm) cc_final: 0.8129 (mt)
REVERT: A 1039 MET cc_start: 0.5900 (pmm) cc_final: 0.4753 (ptt)
REVERT: A 1074 LEU cc_start: 0.8422 (pt) cc_final: 0.8177 (pt)
REVERT: A 1083 LYS cc_start: 0.6144 (pttp) cc_final: 0.5449 (tppt)
REVERT: B   24 ASN cc_start: 0.8235 (t0) cc_final: 0.8006 (t0)
REVERT: C   95 ASN cc_start: 0.6152 (m-40) cc_final: 0.5545 (m-40)
REVERT: D    1 MET cc_start: 0.6510 (tpp) cc_final: 0.6157 (tpp)
REVERT: D   17 GLU cc_start: 0.8450 (pt0) cc_final: 0.8072 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 334
  average time/residue: 0.1237
  time to fit residues: 61.3197
Evaluate side-chains
  228 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 98 optimal weight:    0.1980
   chunk 194 optimal weight:   10.0000
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    0.9990
   overall best weight:    1.6388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 239 HIS
** B  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 HIS
B 204 GLN
** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 108 GLN
** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 131 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.170946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.129921 restraints weight = 27010.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.134211 restraints weight = 13954.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.137056 restraints weight = 9187.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.138810 restraints weight = 7068.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.139962 restraints weight = 6020.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.1494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  16541  Z= 0.170
  Angle     :  0.688  17.403  22532  Z= 0.347
  Chirality :  0.044   0.172   2511
  Planarity :  0.005   0.078   2762
  Dihedral  : 15.562 141.755   2535
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  :  8.03 %
    Favored  : 90.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.90 (0.18), residues: 1911
  helix: -0.01 (0.21), residues: 592
  sheet:  0.01 (0.24), residues: 473
  loop : -1.32 (0.20), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C   5 
 TYR   0.017   0.002   TYR A 397 
 PHE   0.024   0.002   PHE C 215 
 TRP   0.025   0.002   TRP A1166 
 HIS   0.005   0.001   HIS A 475 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (16537)
  covalent geometry    : angle       0.66006 (22520)
  hydrogen bonds       : bond        0.04524 (  726)
  hydrogen bonds       : angle       5.82344 ( 2028)
  metal coordination   : bond        0.01065 (    4)
  metal coordination   : angle       8.38936 (   12)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 246
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 MET cc_start: 0.5432 (pmm) cc_final: 0.4934 (ptt)
REVERT: A  446 ARG cc_start: 0.6925 (tmm160) cc_final: 0.6641 (mmt180)
REVERT: A  549 SER cc_start: 0.8709 (m) cc_final: 0.8445 (p)
REVERT: A  689 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8602 (tt0)
REVERT: A  850 ILE cc_start: 0.8591 (mm) cc_final: 0.8153 (mt)
REVERT: A  906 THR cc_start: 0.8971 (m) cc_final: 0.8493 (p)
REVERT: A  979 LEU cc_start: 0.6747 (mm) cc_final: 0.5846 (tt)
REVERT: A  986 GLN cc_start: 0.5453 (pt0) cc_final: 0.5210 (pp30)
REVERT: A 1039 MET cc_start: 0.5961 (pmm) cc_final: 0.5001 (ptt)
REVERT: A 1083 LYS cc_start: 0.6243 (pttp) cc_final: 0.5448 (tppt)
REVERT: B   12 LEU cc_start: 0.7280 (tp) cc_final: 0.7069 (tp)
REVERT: B  119 MET cc_start: 0.7240 (ppp) cc_final: 0.7013 (ppp)
REVERT: B  199 MET cc_start: 0.6248 (tpt) cc_final: 0.4982 (tpt)
REVERT: C   95 ASN cc_start: 0.6274 (m-40) cc_final: 0.5797 (m-40)
REVERT: C  247 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6912 (tt)
REVERT: C  248 LYS cc_start: 0.8480 (mmtm) cc_final: 0.8235 (mmtm)
REVERT: D   17 GLU cc_start: 0.8628 (pt0) cc_final: 0.8003 (pt0)
REVERT: D   53 ARG cc_start: 0.8162 (mpp80) cc_final: 0.7766 (mtm110)
REVERT: D  210 ARG cc_start: 0.7401 (tpm170) cc_final: 0.7132 (tpm170)
  outliers start: 26
  outliers final: 16
  residues processed: 259
  average time/residue: 0.1279
  time to fit residues: 50.6431
Evaluate side-chains
  242 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 225
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  684 HIS
Chi-restraints excluded: chain A residue  690 LEU
Chi-restraints excluded: chain A residue  708 HIS
Chi-restraints excluded: chain A residue  736 ILE
Chi-restraints excluded: chain A residue 1053 SER
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  247 LEU
Chi-restraints excluded: chain D residue   23 ILE
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  235 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 156 optimal weight:    5.9990
   chunk 143 optimal weight:    0.0670
   chunk 171 optimal weight:    6.9990
   chunk 134 optimal weight:    0.8980
   chunk 146 optimal weight:   10.0000
   chunk 8 optimal weight:    3.9990
   chunk 160 optimal weight:    0.0770
   chunk 22 optimal weight:    0.3980
   chunk 172 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 164 optimal weight:    6.9990
   overall best weight:    0.4476

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 204 GLN
** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 ASN
C 246 HIS
** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 204 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.174161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.133281 restraints weight = 27042.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.137794 restraints weight = 13501.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.140795 restraints weight = 8687.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.142685 restraints weight = 6592.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.143891 restraints weight = 5559.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  16541  Z= 0.111
  Angle     :  0.604  10.525  22532  Z= 0.309
  Chirality :  0.042   0.166   2511
  Planarity :  0.004   0.064   2762
  Dihedral  : 15.416 141.042   2535
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  9.63 %
    Favored  : 88.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.55 (0.19), residues: 1911
  helix:  0.45 (0.21), residues: 595
  sheet:  0.10 (0.24), residues: 494
  loop : -1.20 (0.20), residues: 822

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C   5 
 TYR   0.012   0.001   TYR A 224 
 PHE   0.023   0.002   PHE C 215 
 TRP   0.028   0.002   TRP A1166 
 HIS   0.005   0.001   HIS B 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (16537)
  covalent geometry    : angle       0.59127 (22520)
  hydrogen bonds       : bond        0.03780 (  726)
  hydrogen bonds       : angle       5.33389 ( 2028)
  metal coordination   : bond        0.00390 (    4)
  metal coordination   : angle       5.43926 (   12)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 261
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 MET cc_start: 0.5443 (pmm) cc_final: 0.4878 (ptt)
REVERT: A  310 ARG cc_start: 0.7874 (mmm160) cc_final: 0.7665 (mmm-85)
REVERT: A  446 ARG cc_start: 0.6871 (tmm160) cc_final: 0.6602 (mmt180)
REVERT: A  689 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8539 (tt0)
REVERT: A  850 ILE cc_start: 0.8467 (mm) cc_final: 0.7937 (mt)
REVERT: A  906 THR cc_start: 0.8879 (m) cc_final: 0.8452 (p)
REVERT: A 1039 MET cc_start: 0.6015 (pmm) cc_final: 0.5074 (ptt)
REVERT: A 1083 LYS cc_start: 0.6219 (pttp) cc_final: 0.5474 (tppt)
REVERT: B   12 LEU cc_start: 0.7207 (tp) cc_final: 0.6950 (tp)
REVERT: B  116 MET cc_start: 0.7573 (pmm) cc_final: 0.7256 (ppp)
REVERT: B  139 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7459 (ptp)
REVERT: B  199 MET cc_start: 0.5877 (tpt) cc_final: 0.4653 (tpt)
REVERT: C   20 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7962 (pttp)
REVERT: C   47 LEU cc_start: 0.7545 (pp) cc_final: 0.7234 (tt)
REVERT: C   95 ASN cc_start: 0.6216 (m-40) cc_final: 0.5771 (m-40)
REVERT: C  133 TYR cc_start: 0.7640 (m-10) cc_final: 0.7439 (m-10)
REVERT: C  174 GLU cc_start: 0.7988 (pp20) cc_final: 0.7609 (pm20)
REVERT: D    1 MET cc_start: 0.6412 (tpp) cc_final: 0.6162 (tpp)
REVERT: D   17 GLU cc_start: 0.8603 (pt0) cc_final: 0.7857 (pt0)
REVERT: D  115 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7445 (mm-30)
REVERT: D  150 ASP cc_start: 0.7547 (t0) cc_final: 0.7335 (t70)
REVERT: D  210 ARG cc_start: 0.7352 (tpm170) cc_final: 0.7048 (tpm170)
REVERT: D  244 MET cc_start: 0.6990 (mmm) cc_final: 0.6664 (tpt)
  outliers start: 29
  outliers final: 20
  residues processed: 274
  average time/residue: 0.1347
  time to fit residues: 54.5449
Evaluate side-chains
  248 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 226
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  684 HIS
Chi-restraints excluded: chain A residue  690 LEU
Chi-restraints excluded: chain A residue  708 HIS
Chi-restraints excluded: chain A residue  736 ILE
Chi-restraints excluded: chain A residue 1018 TYR
Chi-restraints excluded: chain A residue 1172 LEU
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain C residue   20 LYS
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  191 GLU
Chi-restraints excluded: chain C residue  241 ILE
Chi-restraints excluded: chain D residue  135 CYS
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  235 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 133 optimal weight:    0.7980
   chunk 0 optimal weight:   20.0000
   chunk 46 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   chunk 100 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 123 optimal weight:   10.0000
   chunk 98 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   chunk 175 optimal weight:    0.8980
   chunk 187 optimal weight:    1.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 HIS
B  71 ASN
B 204 GLN
** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.170499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.128774 restraints weight = 27337.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.133030 restraints weight = 14337.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.135891 restraints weight = 9531.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.137695 restraints weight = 7376.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.138801 restraints weight = 6291.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7157
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  16541  Z= 0.156
  Angle     :  0.645  16.150  22532  Z= 0.321
  Chirality :  0.043   0.165   2511
  Planarity :  0.004   0.077   2762
  Dihedral  : 15.417 141.137   2535
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 12.29 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.46 (0.19), residues: 1911
  helix:  0.52 (0.21), residues: 597
  sheet:  0.18 (0.24), residues: 494
  loop : -1.18 (0.21), residues: 820

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 579 
 TYR   0.022   0.002   TYR A 244 
 PHE   0.019   0.002   PHE B 207 
 TRP   0.026   0.002   TRP A1166 
 HIS   0.009   0.001   HIS B 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (16537)
  covalent geometry    : angle       0.61794 (22520)
  hydrogen bonds       : bond        0.03822 (  726)
  hydrogen bonds       : angle       5.15938 ( 2028)
  metal coordination   : bond        0.00971 (    4)
  metal coordination   : angle       7.98684 (   12)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 232
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 MET cc_start: 0.5360 (pmm) cc_final: 0.5112 (ptp)
REVERT: A  299 MET cc_start: 0.6436 (mmt) cc_final: 0.6131 (mmp)
REVERT: A  446 ARG cc_start: 0.6903 (tmm160) cc_final: 0.6703 (mmt180)
REVERT: A  561 ARG cc_start: 0.7373 (mmp-170) cc_final: 0.7137 (mmp-170)
REVERT: A  684 HIS cc_start: 0.8696 (OUTLIER) cc_final: 0.8208 (t-90)
REVERT: A  689 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8636 (tt0)
REVERT: A  850 ILE cc_start: 0.8479 (mm) cc_final: 0.7983 (mt)
REVERT: A  986 GLN cc_start: 0.5523 (pt0) cc_final: 0.5296 (pp30)
REVERT: A 1039 MET cc_start: 0.5952 (pmm) cc_final: 0.5166 (ptm)
REVERT: A 1083 LYS cc_start: 0.6322 (pttp) cc_final: 0.5532 (tppt)
REVERT: B   12 LEU cc_start: 0.7346 (tp) cc_final: 0.7058 (tp)
REVERT: B  115 GLU cc_start: 0.6512 (pm20) cc_final: 0.6302 (pm20)
REVERT: B  116 MET cc_start: 0.7738 (pmm) cc_final: 0.7404 (ppp)
REVERT: B  199 MET cc_start: 0.6209 (tpt) cc_final: 0.4899 (tpt)
REVERT: C   20 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8188 (pttt)
REVERT: C   47 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7255 (tt)
REVERT: C  133 TYR cc_start: 0.7749 (m-10) cc_final: 0.7535 (m-10)
REVERT: C  246 HIS cc_start: 0.8001 (p90) cc_final: 0.7730 (p-80)
REVERT: C  248 LYS cc_start: 0.8554 (mmtm) cc_final: 0.8294 (mmtm)
REVERT: D   17 GLU cc_start: 0.8603 (pt0) cc_final: 0.7895 (pt0)
REVERT: D  115 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7384 (mm-30)
REVERT: D  210 ARG cc_start: 0.7381 (tpm170) cc_final: 0.7104 (tpm170)
  outliers start: 41
  outliers final: 24
  residues processed: 251
  average time/residue: 0.1249
  time to fit residues: 47.6325
Evaluate side-chains
  237 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 210
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  684 HIS
Chi-restraints excluded: chain A residue  690 LEU
Chi-restraints excluded: chain A residue  708 HIS
Chi-restraints excluded: chain A residue  736 ILE
Chi-restraints excluded: chain A residue 1018 TYR
Chi-restraints excluded: chain A residue 1053 SER
Chi-restraints excluded: chain A residue 1172 LEU
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain C residue   20 LYS
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  191 GLU
Chi-restraints excluded: chain C residue  241 ILE
Chi-restraints excluded: chain D residue   23 ILE
Chi-restraints excluded: chain D residue  135 CYS
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  236 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 15 optimal weight:    0.4980
   chunk 191 optimal weight:   10.0000
   chunk 142 optimal weight:    9.9990
   chunk 81 optimal weight:    0.9990
   chunk 91 optimal weight:    6.9990
   chunk 160 optimal weight:    0.7980
   chunk 104 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 174 optimal weight:    6.9990
   overall best weight:    1.0586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 511 HIS
B  38 GLN
B 131 GLN
B 204 GLN
** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 131 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.170493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.129551 restraints weight = 27049.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.133827 restraints weight = 13922.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.136677 restraints weight = 9104.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.138444 restraints weight = 6987.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.139579 restraints weight = 5932.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
moved from start:          0.2287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16541  Z= 0.129
  Angle     :  0.614  14.157  22532  Z= 0.309
  Chirality :  0.042   0.166   2511
  Planarity :  0.004   0.077   2762
  Dihedral  : 15.359 141.045   2535
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 14.41 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.40 (0.19), residues: 1911
  helix:  0.62 (0.21), residues: 597
  sheet:  0.21 (0.23), residues: 501
  loop : -1.21 (0.21), residues: 813

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 579 
 TYR   0.018   0.001   TYR A 458 
 PHE   0.023   0.002   PHE C 215 
 TRP   0.020   0.001   TRP A 369 
 HIS   0.008   0.001   HIS B 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (16537)
  covalent geometry    : angle       0.59258 (22520)
  hydrogen bonds       : bond        0.03596 (  726)
  hydrogen bonds       : angle       4.97146 ( 2028)
  metal coordination   : bond        0.00713 (    4)
  metal coordination   : angle       7.03007 (   12)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 234
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.6092 (tptp) cc_final: 0.5820 (tptt)
REVERT: A  293 ILE cc_start: 0.6538 (OUTLIER) cc_final: 0.6315 (tt)
REVERT: A  684 HIS cc_start: 0.8700 (OUTLIER) cc_final: 0.8237 (t-90)
REVERT: A  689 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8636 (tt0)
REVERT: A  850 ILE cc_start: 0.8457 (mm) cc_final: 0.7980 (mt)
REVERT: A  906 THR cc_start: 0.8973 (m) cc_final: 0.8602 (p)
REVERT: A  986 GLN cc_start: 0.5469 (pt0) cc_final: 0.5243 (pp30)
REVERT: A 1039 MET cc_start: 0.5937 (pmm) cc_final: 0.5462 (ptp)
REVERT: A 1083 LYS cc_start: 0.6332 (pttp) cc_final: 0.5564 (tppt)
REVERT: A 1183 ILE cc_start: 0.6432 (OUTLIER) cc_final: 0.6177 (mm)
REVERT: B   12 LEU cc_start: 0.7279 (tp) cc_final: 0.6987 (tp)
REVERT: B  116 MET cc_start: 0.7725 (pmm) cc_final: 0.7373 (ppp)
REVERT: B  244 MET cc_start: 0.8509 (tmm) cc_final: 0.8268 (tmm)
REVERT: C   20 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8178 (pttt)
REVERT: C   47 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7241 (tt)
REVERT: C  133 TYR cc_start: 0.7767 (m-10) cc_final: 0.7485 (m-10)
REVERT: C  235 LEU cc_start: 0.7178 (pt) cc_final: 0.6234 (tt)
REVERT: C  248 LYS cc_start: 0.8524 (mmtm) cc_final: 0.8048 (mmtm)
REVERT: D   17 GLU cc_start: 0.8592 (pt0) cc_final: 0.7876 (pt0)
REVERT: D  115 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7479 (mm-30)
REVERT: D  210 ARG cc_start: 0.7315 (tpm170) cc_final: 0.6987 (tpm170)
  outliers start: 43
  outliers final: 25
  residues processed: 255
  average time/residue: 0.1280
  time to fit residues: 49.2994
Evaluate side-chains
  246 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 216
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  684 HIS
Chi-restraints excluded: chain A residue  690 LEU
Chi-restraints excluded: chain A residue  708 HIS
Chi-restraints excluded: chain A residue  736 ILE
Chi-restraints excluded: chain A residue 1018 TYR
Chi-restraints excluded: chain A residue 1053 SER
Chi-restraints excluded: chain A residue 1172 LEU
Chi-restraints excluded: chain A residue 1183 ILE
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   38 GLN
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain C residue   20 LYS
Chi-restraints excluded: chain C residue   29 ASP
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  241 ILE
Chi-restraints excluded: chain D residue   11 ILE
Chi-restraints excluded: chain D residue   23 ILE
Chi-restraints excluded: chain D residue  135 CYS
Chi-restraints excluded: chain D residue  221 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 162 optimal weight:    1.9990
   chunk 165 optimal weight:    8.9990
   chunk 92 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 67 optimal weight:    0.1980
   chunk 141 optimal weight:    0.9980
   chunk 127 optimal weight:    0.9980
   chunk 86 optimal weight:   10.0000
   chunk 91 optimal weight:    6.9990
   chunk 121 optimal weight:    5.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 204 GLN
** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 108 GLN
** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.170865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.129832 restraints weight = 26942.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.135511 restraints weight = 14467.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.136773 restraints weight = 8555.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.137309 restraints weight = 6936.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.137806 restraints weight = 6936.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7176
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  16541  Z= 0.129
  Angle     :  0.623  13.920  22532  Z= 0.311
  Chirality :  0.042   0.163   2511
  Planarity :  0.004   0.078   2762
  Dihedral  : 15.330 141.009   2535
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.53 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.19), residues: 1911
  helix:  0.61 (0.21), residues: 597
  sheet:  0.25 (0.24), residues: 492
  loop : -1.19 (0.21), residues: 822

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 579 
 TYR   0.018   0.001   TYR A 458 
 PHE   0.024   0.002   PHE A 335 
 TRP   0.021   0.001   TRP A 369 
 HIS   0.007   0.001   HIS B 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (16537)
  covalent geometry    : angle       0.60309 (22520)
  hydrogen bonds       : bond        0.03583 (  726)
  hydrogen bonds       : angle       4.90976 ( 2028)
  metal coordination   : bond        0.00608 (    4)
  metal coordination   : angle       6.87591 (   12)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 225
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 TYR cc_start: 0.6150 (OUTLIER) cc_final: 0.5720 (p90)
REVERT: A  119 PHE cc_start: 0.8406 (t80) cc_final: 0.8126 (t80)
REVERT: A  294 MET cc_start: 0.4293 (ptt) cc_final: 0.4014 (ptt)
REVERT: A  299 MET cc_start: 0.6358 (mmt) cc_final: 0.6122 (mmt)
REVERT: A  446 ARG cc_start: 0.6501 (mmt180) cc_final: 0.6217 (mmt180)
REVERT: A  561 ARG cc_start: 0.7172 (mmp-170) cc_final: 0.6859 (mmp-170)
REVERT: A  684 HIS cc_start: 0.8768 (OUTLIER) cc_final: 0.8322 (t-90)
REVERT: A  689 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8636 (tt0)
REVERT: A  850 ILE cc_start: 0.8471 (mm) cc_final: 0.8101 (mt)
REVERT: A  906 THR cc_start: 0.8982 (m) cc_final: 0.8599 (p)
REVERT: A  986 GLN cc_start: 0.5569 (pt0) cc_final: 0.5312 (pp30)
REVERT: A 1024 MET cc_start: 0.6411 (ppp) cc_final: 0.5713 (ppp)
REVERT: A 1039 MET cc_start: 0.5945 (pmm) cc_final: 0.5633 (ptp)
REVERT: A 1083 LYS cc_start: 0.6344 (pttp) cc_final: 0.5576 (tppt)
REVERT: A 1183 ILE cc_start: 0.6430 (OUTLIER) cc_final: 0.6194 (mm)
REVERT: B   12 LEU cc_start: 0.7298 (tp) cc_final: 0.7083 (tp)
REVERT: B  116 MET cc_start: 0.7716 (pmm) cc_final: 0.7396 (ppp)
REVERT: B  244 MET cc_start: 0.8438 (tmm) cc_final: 0.8196 (tmm)
REVERT: C   47 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7230 (tt)
REVERT: C  108 GLN cc_start: 0.7380 (mm110) cc_final: 0.6369 (tp40)
REVERT: C  133 TYR cc_start: 0.7834 (m-10) cc_final: 0.7526 (m-10)
REVERT: C  153 HIS cc_start: 0.7746 (t70) cc_final: 0.7528 (t70)
REVERT: C  235 LEU cc_start: 0.7240 (pt) cc_final: 0.6266 (tt)
REVERT: D   17 GLU cc_start: 0.8589 (pt0) cc_final: 0.7845 (pt0)
REVERT: D  115 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7476 (mm-30)
REVERT: D  210 ARG cc_start: 0.7344 (tpm170) cc_final: 0.7013 (tpm170)
REVERT: D  244 MET cc_start: 0.7378 (mmm) cc_final: 0.7091 (tpt)
  outliers start: 43
  outliers final: 30
  residues processed: 252
  average time/residue: 0.1252
  time to fit residues: 47.3944
Evaluate side-chains
  244 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 210
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue  103 TYR
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  684 HIS
Chi-restraints excluded: chain A residue  690 LEU
Chi-restraints excluded: chain A residue  708 HIS
Chi-restraints excluded: chain A residue  736 ILE
Chi-restraints excluded: chain A residue  820 MET
Chi-restraints excluded: chain A residue 1018 TYR
Chi-restraints excluded: chain A residue 1053 SER
Chi-restraints excluded: chain A residue 1172 LEU
Chi-restraints excluded: chain A residue 1183 ILE
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   64 ARG
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain C residue   29 ASP
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  191 GLU
Chi-restraints excluded: chain C residue  241 ILE
Chi-restraints excluded: chain C residue  246 HIS
Chi-restraints excluded: chain D residue   23 ILE
Chi-restraints excluded: chain D residue  135 CYS
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  236 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 166 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 189 optimal weight:    0.1980
   chunk 39 optimal weight:    0.0980
   chunk 64 optimal weight:    7.9990
   chunk 184 optimal weight:    5.9990
   chunk 92 optimal weight:    0.9980
   chunk 164 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.6182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 245 ASN
** B  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 131 GLN
B 204 GLN
** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 ASN
D 246 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.172322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.131668 restraints weight = 26627.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.136788 restraints weight = 14268.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.138352 restraints weight = 8574.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.138635 restraints weight = 7281.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.139002 restraints weight = 6991.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7147
moved from start:          0.2590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16541  Z= 0.112
  Angle     :  0.612  18.990  22532  Z= 0.305
  Chirality :  0.042   0.162   2511
  Planarity :  0.004   0.078   2762
  Dihedral  : 15.243 140.743   2535
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 16.30 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.19), residues: 1911
  helix:  0.61 (0.21), residues: 598
  sheet:  0.27 (0.24), residues: 504
  loop : -1.16 (0.21), residues: 809

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 579 
 TYR   0.020   0.001   TYR A 458 
 PHE   0.017   0.001   PHE A 335 
 TRP   0.023   0.001   TRP A 369 
 HIS   0.008   0.001   HIS B 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (16537)
  covalent geometry    : angle       0.59970 (22520)
  hydrogen bonds       : bond        0.03432 (  726)
  hydrogen bonds       : angle       4.80769 ( 2028)
  metal coordination   : bond        0.00365 (    4)
  metal coordination   : angle       5.26634 (   12)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 235
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  359 MET cc_start: 0.6350 (ptt) cc_final: 0.6060 (ptt)
REVERT: A  447 MET cc_start: 0.8609 (tpp) cc_final: 0.8270 (tpp)
REVERT: A  561 ARG cc_start: 0.7219 (mmp-170) cc_final: 0.6971 (mmp-170)
REVERT: A  684 HIS cc_start: 0.8770 (OUTLIER) cc_final: 0.8314 (t-90)
REVERT: A  689 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8638 (tt0)
REVERT: A  850 ILE cc_start: 0.8370 (mm) cc_final: 0.7839 (mt)
REVERT: A  906 THR cc_start: 0.8939 (m) cc_final: 0.8558 (p)
REVERT: A  986 GLN cc_start: 0.5489 (pt0) cc_final: 0.5269 (pp30)
REVERT: A 1039 MET cc_start: 0.5924 (pmm) cc_final: 0.5628 (ptp)
REVERT: A 1083 LYS cc_start: 0.6349 (pttp) cc_final: 0.5574 (tppt)
REVERT: A 1183 ILE cc_start: 0.6463 (OUTLIER) cc_final: 0.6252 (mm)
REVERT: B   12 LEU cc_start: 0.7284 (tp) cc_final: 0.7022 (tp)
REVERT: B  116 MET cc_start: 0.7652 (pmm) cc_final: 0.7260 (ppp)
REVERT: B  244 MET cc_start: 0.8394 (tmm) cc_final: 0.8170 (tmm)
REVERT: C   47 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7272 (tt)
REVERT: C  133 TYR cc_start: 0.7794 (m-10) cc_final: 0.7492 (m-10)
REVERT: C  153 HIS cc_start: 0.7800 (t70) cc_final: 0.7544 (t70)
REVERT: C  235 LEU cc_start: 0.7260 (pt) cc_final: 0.6257 (tt)
REVERT: D   17 GLU cc_start: 0.8554 (pt0) cc_final: 0.7800 (pt0)
REVERT: D  115 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7392 (mm-30)
REVERT: D  210 ARG cc_start: 0.7365 (tpm170) cc_final: 0.7085 (tpm170)
REVERT: D  244 MET cc_start: 0.7419 (mmm) cc_final: 0.7163 (tpt)
  outliers start: 37
  outliers final: 27
  residues processed: 254
  average time/residue: 0.1187
  time to fit residues: 45.5461
Evaluate side-chains
  244 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 214
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  684 HIS
Chi-restraints excluded: chain A residue  708 HIS
Chi-restraints excluded: chain A residue  736 ILE
Chi-restraints excluded: chain A residue 1018 TYR
Chi-restraints excluded: chain A residue 1053 SER
Chi-restraints excluded: chain A residue 1141 ILE
Chi-restraints excluded: chain A residue 1172 LEU
Chi-restraints excluded: chain A residue 1183 ILE
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   64 ARG
Chi-restraints excluded: chain B residue   81 CYS
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  191 GLU
Chi-restraints excluded: chain C residue  241 ILE
Chi-restraints excluded: chain C residue  246 HIS
Chi-restraints excluded: chain D residue  135 CYS
Chi-restraints excluded: chain D residue  236 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 58 optimal weight:    0.2980
   chunk 46 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 162 optimal weight:    1.9990
   chunk 158 optimal weight:    0.2980
   chunk 81 optimal weight:    0.0050
   chunk 124 optimal weight:    7.9990
   chunk 131 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 146 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.4194

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 131 GLN
B 204 GLN
** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.173145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.132758 restraints weight = 26632.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.137706 restraints weight = 14417.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.139044 restraints weight = 8610.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.139689 restraints weight = 7478.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.139939 restraints weight = 6920.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.2740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16541  Z= 0.113
  Angle     :  0.627  18.865  22532  Z= 0.314
  Chirality :  0.042   0.162   2511
  Planarity :  0.004   0.083   2762
  Dihedral  : 15.184 140.455   2535
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 16.95 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.30 (0.19), residues: 1911
  helix:  0.68 (0.21), residues: 597
  sheet:  0.31 (0.24), residues: 504
  loop : -1.15 (0.21), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 579 
 TYR   0.021   0.001   TYR A 458 
 PHE   0.019   0.001   PHE A 119 
 TRP   0.019   0.001   TRP A 369 
 HIS   0.004   0.001   HIS D 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (16537)
  covalent geometry    : angle       0.61856 (22520)
  hydrogen bonds       : bond        0.03311 (  726)
  hydrogen bonds       : angle       4.72906 ( 2028)
  metal coordination   : bond        0.00342 (    4)
  metal coordination   : angle       4.50055 (   12)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 232
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.6286 (tptp) cc_final: 0.5859 (tptt)
REVERT: A  238 ILE cc_start: 0.8654 (mm) cc_final: 0.8250 (mm)
REVERT: A  447 MET cc_start: 0.8646 (tpp) cc_final: 0.8261 (tpp)
REVERT: A  561 ARG cc_start: 0.7186 (mmp-170) cc_final: 0.6924 (mmp-170)
REVERT: A  684 HIS cc_start: 0.8714 (OUTLIER) cc_final: 0.8264 (t-90)
REVERT: A  689 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8641 (tt0)
REVERT: A  850 ILE cc_start: 0.8312 (mm) cc_final: 0.8097 (mm)
REVERT: A  906 THR cc_start: 0.8896 (m) cc_final: 0.8573 (p)
REVERT: A 1039 MET cc_start: 0.5929 (pmm) cc_final: 0.5405 (ptm)
REVERT: A 1083 LYS cc_start: 0.6387 (pttp) cc_final: 0.5652 (tppt)
REVERT: B   12 LEU cc_start: 0.7314 (tp) cc_final: 0.7060 (tp)
REVERT: B   24 ASN cc_start: 0.8239 (t0) cc_final: 0.8024 (t0)
REVERT: B  115 GLU cc_start: 0.6126 (pp20) cc_final: 0.5752 (pp20)
REVERT: B  116 MET cc_start: 0.7587 (pmm) cc_final: 0.7168 (ppp)
REVERT: B  117 LYS cc_start: 0.7735 (ptpt) cc_final: 0.7381 (ptpt)
REVERT: B  244 MET cc_start: 0.8412 (tmm) cc_final: 0.8208 (tmm)
REVERT: C   47 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7282 (tt)
REVERT: C  116 MET cc_start: 0.6288 (tpt) cc_final: 0.5985 (tpt)
REVERT: C  133 TYR cc_start: 0.7730 (m-10) cc_final: 0.7508 (m-10)
REVERT: C  153 HIS cc_start: 0.7759 (t70) cc_final: 0.7517 (t70)
REVERT: D   17 GLU cc_start: 0.8493 (pt0) cc_final: 0.7747 (pt0)
REVERT: D  115 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7371 (mm-30)
REVERT: D  210 ARG cc_start: 0.7419 (tpm170) cc_final: 0.7146 (tpm170)
REVERT: D  244 MET cc_start: 0.7452 (mmm) cc_final: 0.7019 (tpt)
  outliers start: 35
  outliers final: 23
  residues processed: 253
  average time/residue: 0.1288
  time to fit residues: 49.1793
Evaluate side-chains
  235 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 210
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  294 MET
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  684 HIS
Chi-restraints excluded: chain A residue  708 HIS
Chi-restraints excluded: chain A residue  736 ILE
Chi-restraints excluded: chain A residue 1018 TYR
Chi-restraints excluded: chain A residue 1053 SER
Chi-restraints excluded: chain A residue 1141 ILE
Chi-restraints excluded: chain A residue 1172 LEU
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   64 ARG
Chi-restraints excluded: chain B residue   76 SER
Chi-restraints excluded: chain B residue   81 CYS
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain D residue  135 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 184 optimal weight:    8.9990
   chunk 42 optimal weight:    0.6980
   chunk 4 optimal weight:   10.0000
   chunk 153 optimal weight:    3.9990
   chunk 168 optimal weight:    5.9990
   chunk 188 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 173 optimal weight:    6.9990
   chunk 170 optimal weight:    4.9990
   chunk 160 optimal weight:    0.0670
   overall best weight:    1.0920

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 131 GLN
B 204 GLN
** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.171024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.132074 restraints weight = 26800.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.135458 restraints weight = 14431.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.136768 restraints weight = 8726.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.137619 restraints weight = 7561.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.137842 restraints weight = 7287.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7160
moved from start:          0.2832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  16541  Z= 0.134
  Angle     :  0.664  19.195  22532  Z= 0.327
  Chirality :  0.043   0.184   2511
  Planarity :  0.004   0.080   2762
  Dihedral  : 15.189 140.530   2535
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 17.19 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.19), residues: 1911
  helix:  0.69 (0.21), residues: 595
  sheet:  0.20 (0.24), residues: 496
  loop : -1.12 (0.21), residues: 820

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG A 579 
 TYR   0.019   0.002   TYR A 458 
 PHE   0.027   0.002   PHE D 215 
 TRP   0.025   0.001   TRP A 369 
 HIS   0.006   0.001   HIS C 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (16537)
  covalent geometry    : angle       0.64785 (22520)
  hydrogen bonds       : bond        0.03483 (  726)
  hydrogen bonds       : angle       4.74309 ( 2028)
  metal coordination   : bond        0.00670 (    4)
  metal coordination   : angle       6.36817 (   12)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 215
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
REVERT: A  238 ILE cc_start: 0.8779 (mm) cc_final: 0.8394 (mm)
REVERT: A  447 MET cc_start: 0.8635 (tpp) cc_final: 0.8273 (tpp)
REVERT: A  495 LYS cc_start: 0.6948 (OUTLIER) cc_final: 0.6668 (ptpt)
REVERT: A  684 HIS cc_start: 0.8725 (OUTLIER) cc_final: 0.8295 (t-90)
REVERT: A  685 ARG cc_start: 0.8154 (mtp-110) cc_final: 0.7709 (ttt-90)
REVERT: A  689 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8606 (tt0)
REVERT: A  906 THR cc_start: 0.8995 (m) cc_final: 0.8643 (p)
REVERT: A  986 GLN cc_start: 0.5531 (pt0) cc_final: 0.5318 (pp30)
REVERT: A 1024 MET cc_start: 0.5675 (ppp) cc_final: 0.5214 (ppp)
REVERT: A 1039 MET cc_start: 0.6020 (pmm) cc_final: 0.5615 (ptm)
REVERT: A 1083 LYS cc_start: 0.6446 (pttp) cc_final: 0.5659 (tppt)
REVERT: B   12 LEU cc_start: 0.7392 (tp) cc_final: 0.7136 (tp)
REVERT: B   24 ASN cc_start: 0.8252 (t0) cc_final: 0.8011 (t0)
REVERT: B  116 MET cc_start: 0.7725 (pmm) cc_final: 0.7272 (ppp)
REVERT: B  117 LYS cc_start: 0.7770 (ptpt) cc_final: 0.7377 (ptpt)
REVERT: B  199 MET cc_start: 0.6196 (tpt) cc_final: 0.4828 (tpt)
REVERT: C   47 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7167 (tt)
REVERT: C  133 TYR cc_start: 0.7732 (m-10) cc_final: 0.7517 (m-10)
REVERT: C  153 HIS cc_start: 0.7783 (t70) cc_final: 0.7547 (t70)
REVERT: D   17 GLU cc_start: 0.8496 (pt0) cc_final: 0.7839 (pt0)
REVERT: D  115 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7384 (mm-30)
REVERT: D  210 ARG cc_start: 0.7416 (tpm170) cc_final: 0.7068 (tpm170)
REVERT: D  244 MET cc_start: 0.7472 (mmm) cc_final: 0.7027 (tpt)
  outliers start: 30
  outliers final: 25
  residues processed: 233
  average time/residue: 0.1250
  time to fit residues: 43.7717
Evaluate side-chains
  236 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 208
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  294 MET
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  495 LYS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  684 HIS
Chi-restraints excluded: chain A residue  708 HIS
Chi-restraints excluded: chain A residue  736 ILE
Chi-restraints excluded: chain A residue 1018 TYR
Chi-restraints excluded: chain A residue 1053 SER
Chi-restraints excluded: chain A residue 1172 LEU
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   64 ARG
Chi-restraints excluded: chain B residue   76 SER
Chi-restraints excluded: chain B residue   81 CYS
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain D residue  128 ILE
Chi-restraints excluded: chain D residue  135 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 190 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   chunk 155 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9990
   chunk 175 optimal weight:    0.0970
   chunk 176 optimal weight:    0.9980
   chunk 161 optimal weight:    0.6980
   chunk 184 optimal weight:    4.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 131 GLN
B 204 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.172034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.132803 restraints weight = 26659.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.136741 restraints weight = 14336.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.137863 restraints weight = 8669.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.138897 restraints weight = 7670.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.139422 restraints weight = 7304.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
moved from start:          0.2903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  16541  Z= 0.122
  Angle     :  0.659  19.776  22532  Z= 0.325
  Chirality :  0.042   0.178   2511
  Planarity :  0.004   0.077   2762
  Dihedral  : 15.157 140.513   2535
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 17.25 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.19), residues: 1911
  helix:  0.75 (0.21), residues: 590
  sheet:  0.18 (0.24), residues: 501
  loop : -1.09 (0.21), residues: 820

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 579 
 TYR   0.021   0.001   TYR A 458 
 PHE   0.027   0.002   PHE D 215 
 TRP   0.025   0.001   TRP A 369 
 HIS   0.005   0.001   HIS D 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (16537)
  covalent geometry    : angle       0.64549 (22520)
  hydrogen bonds       : bond        0.03395 (  726)
  hydrogen bonds       : angle       4.71513 ( 2028)
  metal coordination   : bond        0.00498 (    4)
  metal coordination   : angle       5.78475 (   12)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 217
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 ILE cc_start: 0.8738 (mm) cc_final: 0.8361 (mm)
REVERT: A  447 MET cc_start: 0.8604 (tpp) cc_final: 0.8302 (tpp)
REVERT: A  495 LYS cc_start: 0.6858 (OUTLIER) cc_final: 0.6638 (ptpt)
REVERT: A  561 ARG cc_start: 0.7211 (mmp-170) cc_final: 0.6976 (mmp-170)
REVERT: A  684 HIS cc_start: 0.8737 (OUTLIER) cc_final: 0.8316 (t-90)
REVERT: A  685 ARG cc_start: 0.8144 (mtp-110) cc_final: 0.7700 (ttt-90)
REVERT: A  689 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8592 (tt0)
REVERT: A  906 THR cc_start: 0.8990 (m) cc_final: 0.8676 (p)
REVERT: A 1031 GLU cc_start: 0.7618 (pm20) cc_final: 0.7179 (tp30)
REVERT: A 1039 MET cc_start: 0.5996 (pmm) cc_final: 0.5702 (ptm)
REVERT: A 1083 LYS cc_start: 0.6421 (pttp) cc_final: 0.5668 (tppt)
REVERT: B   12 LEU cc_start: 0.7401 (tp) cc_final: 0.7146 (tp)
REVERT: B   24 ASN cc_start: 0.8219 (t0) cc_final: 0.7995 (t0)
REVERT: B  116 MET cc_start: 0.7639 (pmm) cc_final: 0.7237 (ppp)
REVERT: B  117 LYS cc_start: 0.7703 (ptpt) cc_final: 0.7346 (ptpt)
REVERT: C   47 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7154 (tt)
REVERT: C  133 TYR cc_start: 0.7711 (m-10) cc_final: 0.7493 (m-10)
REVERT: C  153 HIS cc_start: 0.7784 (t70) cc_final: 0.7547 (t70)
REVERT: C  238 GLU cc_start: 0.7248 (tp30) cc_final: 0.6937 (tp30)
REVERT: D   17 GLU cc_start: 0.8472 (pt0) cc_final: 0.7923 (pt0)
REVERT: D   49 GLN cc_start: 0.7692 (tm-30) cc_final: 0.7421 (tm-30)
REVERT: D  115 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7357 (mm-30)
REVERT: D  210 ARG cc_start: 0.7410 (tpm170) cc_final: 0.7118 (tpm170)
REVERT: D  244 MET cc_start: 0.7419 (mmm) cc_final: 0.7017 (tpt)
  outliers start: 31
  outliers final: 24
  residues processed: 237
  average time/residue: 0.1251
  time to fit residues: 44.4591
Evaluate side-chains
  239 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 212
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  495 LYS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  684 HIS
Chi-restraints excluded: chain A residue  708 HIS
Chi-restraints excluded: chain A residue  736 ILE
Chi-restraints excluded: chain A residue 1018 TYR
Chi-restraints excluded: chain A residue 1053 SER
Chi-restraints excluded: chain A residue 1172 LEU
Chi-restraints excluded: chain A residue 1183 ILE
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   64 ARG
Chi-restraints excluded: chain B residue   76 SER
Chi-restraints excluded: chain B residue   81 CYS
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain D residue  135 CYS
Chi-restraints excluded: chain D residue  236 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 153 optimal weight:    0.9990
   chunk 122 optimal weight:    2.9990
   chunk 128 optimal weight:    5.9990
   chunk 145 optimal weight:   10.0000
   chunk 143 optimal weight:    7.9990
   chunk 116 optimal weight:    0.0370
   chunk 157 optimal weight:    0.0970
   chunk 189 optimal weight:    3.9990
   chunk 176 optimal weight:    9.9990
   overall best weight:    0.5658

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
** B  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 131 GLN
B 204 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.173138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.133076 restraints weight = 26855.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.138124 restraints weight = 14805.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.139710 restraints weight = 8740.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.140140 restraints weight = 6975.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.140661 restraints weight = 7082.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7135
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  16541  Z= 0.117
  Angle     :  0.652  19.963  22532  Z= 0.322
  Chirality :  0.042   0.170   2511
  Planarity :  0.004   0.075   2762
  Dihedral  : 15.114 140.321   2535
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 17.66 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (0.19), residues: 1911
  helix:  0.80 (0.21), residues: 589
  sheet:  0.25 (0.24), residues: 495
  loop : -1.04 (0.21), residues: 827

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 579 
 TYR   0.021   0.001   TYR A 458 
 PHE   0.022   0.001   PHE B 207 
 TRP   0.022   0.001   TRP A 369 
 HIS   0.004   0.001   HIS A 688 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (16537)
  covalent geometry    : angle       0.64097 (22520)
  hydrogen bonds       : bond        0.03324 (  726)
  hydrogen bonds       : angle       4.68850 ( 2028)
  metal coordination   : bond        0.00412 (    4)
  metal coordination   : angle       5.11935 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2750.63 seconds
wall clock time: 48 minutes 20.11 seconds (2900.11 seconds total)